[gmx-users] temperature shooting up

Mark Abraham Mark.Abraham at anu.edu.au
Thu Nov 9 02:08:13 CET 2006

Cherry Y. Yates wrote:
> Dear Mark,
> Thanks for your help. Actually I did separate runs for flexible and 
> rigid models, and didn't use the equilibrated flexible structure to 
> start with rigid model calculations. But the starting configurations are 
> the same. 

Oh OK - but the same kind of problem can arise if your starting 
configuration doesn't match the constraints of the rigid model.

> So do you mean I need to reduce the T-coupling time? 

See section 3.4.5 of the manual. The smaller the T-coupling time, the 
"harder" the T-coupling constraint is.

> If the 
> initial water geometry is not the same as the rigid model, does the 
> program will "enforce" that geometry for water molecules, or to "relax" 
> water molecure towards it?

As I said last time,

>     It would be simpler ... to do energy minimization to correct any geometries
>     before starting MD simulations.

I've never needed to do this, so can't help with details, but it may be 
necessary for this EM to use a solvent molecule .itp that has real 
bonded functions rather than constraints. Thus this EM is actually doing 
the geometry correction, and the geometry constraint algorithms for MD 
will work as you'd hope.


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